Mulitple point density clouds - intersecting each other
I think you can solve this by using either one of 2 workarounds.

Scaling clouds domain by Z axis

This is kind of lazy solution, which assumes scaling domain cube of the fluffy clouds (those everywhere in the bottom). After domain is no longer intersecting with clouds in the foreground (left / right), there's no intersection.



Processing rendered OpenEXR images


Start with moving fluffy clouds (those in the bottom) with their domain to separate layer (assuming light sources are on a layer turned on in any case). Set up output format as OpenEXR Multilayer. 
Render and save image. Do the same with big clouds on the left and right (so that they were moved together to the same layer). 
Having 2 .exr images, you can import them in another scene, delete RenderLayers node to render only from compositor and mix clouds with AlphaOver node (make sure Channels of the image to draw is set to Color and Alhpa).



Rendered clouds (with and without black layer added for transparency demonstration):


The result is the same for both solutions